A brain image database for structure/function analysis

BACKGROUND AND PURPOSE

Lesion-deficit-based structure-function analysis has traditionally been empirical and nonquantitative. Our purpose was to establish a new brain image database (BRAID) that allows the statistical correlation of brain functional measures with anatomic lesions revealed by clinical brain images.

METHODS

Data on 303 participants in the MR Feasibility Study of the Cardiovascular Health Study were tested for lesion/deficit correlations. Functional data were derived from a limited neurologic examination performed at the time of the MR examination. Image data included 3D lesion descriptions derived from the MR examinations by hand segmentation. MR images were normalized in-plane using local, linear Talairach normalization. A database was implemented to support spatial data structures and associated geometric and statistical operations. The database stored the segmented lesions, patient functional scores, and several anatomic atlases. Lesion-deficit association was sought by contingency testing (chi2-test) for every possible combination of each neurologic variable and each labeled atlas structure. Significant associations that confirmed accepted lesion-deficit relationships were sought.

RESULTS

Two-hundred thirty-five infarctlike lesions in 117 subjects were viewed collectively after mapping into Talairach cartesian coordinates. Anatomic structures most strongly correlated with neurologic deficits tended to be situated in anatomically appropriate areas. For example, infarctlike lesions associated with visual field defects were correlated with structures in contralateral occipital structures, including the optic radiations and occipital gyri.

CONCLUSION

Known lesion-deficit correlations can be established by a database using a standard coordinate system for representing spatial data and incorporating functional and structural data together with appropriate query mechanisms. Improvements and further applications of this methodology may provide a powerful technique for uncovering new structure-function relationships.

GDB: the Human Genome Database

The Genome Database (GDB, http://www.gdb.org ) is a public repository of data on human genes, clones, STSs, polymorphisms and maps. GDB entries are highly cross-linked to each other, to literature citations and to entries in other databases, including the sequence databases, OMIM, and the Mouse Genome Database. Mapping data from large genome centers and smaller mapping efforts are added to GDB on an ongoing basis. The database can be searched by a variety of methods, ranging from keyword searches to complex queries. Major functionality extensions in the last year include the ongoing computation of integrated human genome maps, called Comprehensive Maps, and the use of those maps to support positional queries and graphic displays. The capabilities of the GDB map viewer (Mapview) have been extended to include map printing and the graphical display of ad hoc query results. The HUGO Nomenclature Committee continues to curate the proposed and official gene symbols and related data in collaboration with GDB. As genome research shifts its emphasis from mapping to sequencing and functional analysis, the scope of the GDB schema is being extended. We are in the process of adding representations of gene function and expression, and improving our representation of human polymorphism and mutation.

The GDB Human Genome Database Anno 1997

The value of the Genome Database (GDB) for the human genome research community has been greatly increased since the release of version 6. 0 last year. Thanks to the introduction of significant technical improvements, GDB has seen dramatic growth in the type and volume of information stored in the database. This article summarizes the types of data that are now available in the Genome Database, demonstrates how the database is interconnected with other biomedical resources on the World Wide Web, discusses how researchers can contribute new or updated information to the database, and describes our current efforts as well as planned improvements for the future.

Improvements to the GDB Human Genome Data Base

Version 6.0 of the Human Genome Data Base introduces a number of significant improvements over previous releases of GDB. The most important of these are revised data representations for genes and genomic maps and a new curatorial model for the database. GDB 6.0 is the first major genomic database to provide read/write access directly to the scientific community, including capabilities for third-party annotation. The revised database can represent all major categories of genetic and physical maps, along with the underlying order and distance information used to construct them. The improved representation permits more sophisticated map queries to be posed and supports the graphical display of maps. In addition the new GDB has a richer model for gene information, better suited for supporting cross-references to databases describing gene function, structure, products, expression and associated phenotypes.